RESUMO
Subterranean rodents of the genus Ctenomys (tuco-tucos) are endemic to South America and have experienced relatively recent radiation. There are about 67 recognized species that originated in approximately 1-2 MY. They stand out for their species richness, extraordinary chromosomal diversity, and wide range of habitat they occupy in the continent. Phylogenetic relationships among species of tuco-tucos have been challenging to resolve. Groups of closely-related species have been suggested, but their relationships must be resolved. This study estimates the phylogeny of the genus using massive sequencing, generating thousands of independent molecular markers obtained by RADseq, with a taxonomic sampling that includes 66% of the recognized species. The sequences obtained were mapped against the C. sociabilis genome, recovering up to 1,215 widely shared RAD loci with more than 19,000 polymorphic sites. Our new phylogenetic hypothesis corroborated the species groups previously proposed with cytochrome b gene sequences and provided a much greater resolution of the relationships among species groups. The frater group is sister to all other tuco-tucos, whereas some of the earlierliest proposals placed the sociabilis group as sister to all other tuco-tucos. Ctenomys leucodon, previously proposed as an independent lineage, is associated with the frater group with moderate statistical support. The magellanicus and mendocinus are sister groups in a major clade formed by the boliviensis, talarum, tucumanus, torquatus, and opimus groups. Ctenomys viperinus, included in the phylogeny for the first time, belongs to the tucumanus group. This multi-locus phylogenetic hypothesis provides insights into the historical biogeography of understanding this highly diverse genus.
Assuntos
Especiação Genética , Filogenia , Roedores , Animais , Roedores/genética , Roedores/classificação , Análise de Sequência de DNA , Genoma/genética , América do Sul , GenômicaRESUMO
Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.
Assuntos
Genoma , Cromossomos Sexuais , Humanos , Animais , Reprodutibilidade dos Testes , Genoma/genética , Cromossomos Sexuais/genética , Cromossomo Y , Genômica , Mamíferos/genéticaRESUMO
BACKGROUND: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species. RESULTS: We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million years ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance. CONCLUSIONS: Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time-calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.
Assuntos
Peixes/classificação , Filogenia , Animais , Regiões Antárticas , Sequência de Bases , Calibragem , Loci Gênicos , Marcadores Genéticos , Variação Genética , Genoma , Haplótipos/genética , Funções Verossimilhança , Mitocôndrias/genética , Filogeografia , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA , Especificidade da Espécie , Fatores de TempoRESUMO
Different hypotheses attempt to explain how different stages of organisms with complex life cycles respond to environmental changes. Most studies have focused at the among-species level showing similar responses to temperature throughout ontogeny. However, there is no agreement about the pattern expected at the intraspecific scale where a strong selective effect is expected. In this paper, we studied the effects of thermal treatments on a life history trait (developmental rate) and a physiological trait (metabolic rate) during development in the fruitfly Drosophila buzzatii. First, we estimated the rate of development during larval life (LDR) and the pupal stage (PDR) in flies derived from two natural populations exposed to several thermal treatments. Our results showed that the developmental rate ratio, LDR/PDR, did not vary between populations, and that the effects of thermal treatments were stage specific. Second, we studied the relationship between developmental rate (DR) and metabolic rate (MR) in each life cycle stage. We found that allometric relationships between DR and MR varied throughout ontogeny, a pattern that shed light on the mechanisms responsible for thermal plasticity. We conclude that, although different populations may show developmental rate isomorphy; larvae and pupae may choose alternative "decisions" in terms of life-history evolution and physiological traits when confronted to different thermal environments.